Zhang, X.; Song, J.; Luo, L.; Sun, X.X.; Liu, J. Patterns and Determinants of Synonymous Codon Usage in Mulberry Mosaic Dwarf Associated Virus. Preprints2023, 2023091656. https://doi.org/10.20944/preprints202309.1656.v1
APA Style
Zhang, X., Song, J., Luo, L., Sun, X.X., & Liu, J. (2023). Patterns and Determinants of Synonymous Codon Usage in Mulberry Mosaic Dwarf Associated Virus. Preprints. https://doi.org/10.20944/preprints202309.1656.v1
Chicago/Turabian Style
Zhang, X., Xun xun Sun and JiPing Liu. 2023 "Patterns and Determinants of Synonymous Codon Usage in Mulberry Mosaic Dwarf Associated Virus" Preprints. https://doi.org/10.20944/preprints202309.1656.v1
Abstract
The recently identified Mulberry Mosaic Dwarf-associated Virus (MMDaV), associated with mosaic dwarf symptoms in Chinese mulberry leaves, is a newly discovered member of the Geminiviridae family. The MMDaV genome, a single or twin circular single-stranded DNA molecule measuring approximately 2.5-3.0 kb, encodes five proteins and two hypothetical proteins, including a coat protein (CP) and movement protein (MP). The co-evolutionary dynamics between viral and host codon usage significantly impact viral survival, fitness, immune evasion, and evolutionary pathways. This study applied bioinformatic analyses to examine the codon usage bias in thirty MMDaV genomes collected from mulberry leaves in four distinct Chinese provinces. We aimed to understand the drivers of preferred synonymous codon usage. The Effective Number of Codons (ENC) analysis revealed significant regional variations among MMDaV isolates, allowing their classification into two main categories: the southern China HNZX strain and the eastern China HDZX strain. The codon preference analysis displayed a viral preference for using A/U as the terminal base, indicating a bias towards A/U over G/C. Using a combination of position-specific base composition, ENC-Plot, RP2-Plot, Neutral plot, and correspondence analysis, we found that mutational pressure and natural selection substantially influence codon usage and drive MMDaV evolution. Our findings shed light on the complex interplay between MMDaV and its mulberry host and offer crucial insights into the virus's adaptive and evolutionary mechanisms.
Biology and Life Sciences, Agricultural Science and Agronomy
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
